Our bioinformatician gave me one vcf file (exp1_FPOA_96.vcf) from Illumina HiSeq 3000 with 150 bp paired-end reads and a target insert size of 500 bp (GBS-restriction enzyme) to proceed with further data analyses. I am visiting the following website.
https://grunwaldlab.github.io/Population_Genetics_in_R/gbs_analysis.html
I have installed the following packages in R-studio .
- library(vcfR)
- library(poppr)
- library(ape)
- library(RColorBrewer)
I cant sense I will proceed with this command...
example---
rubi.VCF <- read.vcfR("prubi_gbs.vcf.gz")
please help me how my vcf file will be directed to R.